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Phylogenetic Monte Carlo: Quantifying Uncertainty in Phylogenetic Methods (now on CRAN)
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README.md

README.md

Phylogenetic Monte Carlo

NOTE This package is currently deprecated. See http://www.carlboettiger.info/2013/04/23/we-need-more-object-oriented-design-in-comparative-methods.html

  • Author: Carl Boettiger
  • License: CC0

This package accompanies my publication, with Graham Coop & Peter Ralph (2012) Is your phylogeny Informative? Measuring the power of comparative methods. In Evolution. (doi) (pdf) (arXiv) (code) (data)

Install

The easiest way to install the current release is through the CRAN repository,

install.packages("pmc")

To install the current development version, there are a few options. One is to install devtools package, which will let you install directly from github:

install.packages("devtools")
library(devtools)
install_github("pmc", "cboettig")

The other option is to download the current tarball, put it in the working directory, and then install from R using

install.packages("pmc*.tar.gz", ,type="source", repos=NULL)

Getting Started

The best place to start learning the package commands is to read the package vignette, copy-pasting the examples in as you go. For a faster start, just look at the examples in the function documentation, i.e. ?pmc.

Bug Reports

If you find the package is giving unexpected results, is missing a feature you'd like, or have any other questions about the package, don't hesitate to email me.

You can also file an issue which will provide a record of the bug/request. Posting an issue also automatically sends me an email.

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